River plumes deliver large quantities of nutrients to oligotrophic oceans, often resulting in significant CO 2 drawdown. To determine the relationship between expression of the major gene in carbon fixation (large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, RuBisCO) and CO 2 dynamics, we evaluated rbcL mRNA abundance using novel quantitative PCR assays, phytoplankton cell analyses, photophysiological parameters, and pCO 2 in and around the Mississippi River plume (MRP) in the Gulf of Mexico. Lower salinity (30-32) stations were dominated by rbcL mRNA concentrations from heterokonts, such as diatoms and pelagophytes, which were at least an order of magnitude greater than haptophytes, a-Synechococcus or high-light Prochlorococcus. However, rbcL transcript abundances were similar among these groups at oligotrophic stations (salinity 34-36). Diatom cell counts and heterokont rbcL RNA showed a strong negative correlation to seawater pCO 2 . While Prochlorococcus cells did not exhibit a large difference between low and high pCO 2 water, Prochlorococcus rbcL RNA concentrations had a strong positive correlation to pCO 2 , suggesting a very low level of RuBisCO RNA transcription among Prochlorococcus in the plume waters, possibly due to their relatively poor carbon concentrating mechanisms (CCMs). These results provide molecular evidence that diatom/pelagophyte productivity is largely responsible for the large CO 2 drawdown occurring in the MRP, based on the cooccurrence of elevated RuBisCO gene transcript concentrations from this group and reduced seawater pCO 2 levels. This may partly be due to efficient CCMs that enable heterokont eukaryotes such as diatoms to continue fixing CO 2 in the face of strong CO 2 drawdown. Our work represents the first attempt to relate in situ microbial gene expression to contemporaneous CO 2 flux measurements in the ocean.